def test_one():
Z, symbol = get_atomic_number_symbol(Z=8)
assert Z[0] == 8
assert symbol[0] == 'O'
Z, symbol = get_atomic_number_symbol(symbol='C')
assert Z[0] == 6
assert symbol[0] == 'C'
Z, symbol = get_atomic_number_symbol(Z=10, symbol='Ne')
assert Z[0] == 10
assert symbol[0] == 'Ne'
def test_array():
Z, symbol = get_atomic_number_symbol(Z=[6, 7, 8])
assert_array_equal(Z, [6, 7, 8])
assert_array_equal(symbol, ['C', 'N', 'O'])
Z, symbol = get_atomic_number_symbol(symbol=['Au', 'Ag'])
assert_array_equal(Z, [79, 47])
assert_array_equal(symbol, ['Au', 'Ag'])
Z, symbol = get_atomic_number_symbol(Z=[1, 2, 3], symbol=['B', 'C', 'F'])
assert_array_equal(Z, [5, 6, 9])
assert_array_equal(symbol, ['B', 'C', 'F'])
def repeat(self, rep):
"""Repeat the cells a number of time along each dimension
*rep* argument should be either three value like *(1,2,3)* or
a single value *r* equivalent to *(r,r,r)*."""
if isinstance(rep, int):
rep = np.array((rep, rep, rep, 1))
else:
rep = np.append(rep, 1)
ncells = np.array(self.atoms.index.max()) + 1
x = np.tile(np.reshape(self.x, ncells), rep).flatten()
y = np.tile(np.reshape(self.y, ncells), rep).flatten()
z = np.tile(np.reshape(self.z, ncells), rep).flatten()
Z = np.tile(np.reshape(self.get_atomic_numbers(), ncells), rep).flatten()
miindex = get_miindex(0, ncells * rep)
self.atoms = DataFrame(index=miindex,
columns=['Z', 'symbol',
'x', 'y', 'z'])
self.atoms.Z, self.atoms.symbol = get_atomic_number_symbol(Z=Z)
self.atoms.x = x
self.atoms.y = y
self.atoms.z = z
def repeat(self, rep):
"""Repeat the cells a number of time along each dimension
*rep* argument should be either three value like *(1,2,3)* or
a single value *r* equivalent to *(r,r,r)*."""
if isinstance(rep, int):
rep = np.array((rep, rep, rep, 1))
else:
rep = np.append(rep, 1)
ncells = np.array(self.atoms.index.max()) + 1
x = np.tile(np.reshape(self.x, ncells), rep).flatten()
y = np.tile(np.reshape(self.y, ncells), rep).flatten()
z = np.tile(np.reshape(self.z, ncells), rep).flatten()
Z = np.tile(np.reshape(self.get_atomic_numbers(), ncells),
rep).flatten()
miindex = get_miindex(0, ncells * rep)
self.atoms = DataFrame(index=miindex,
columns=[
'Z', 'symbol', 'x', 'y', 'z', 'cartn_x',
'cartn_y', 'cartn_z'
])
self.atoms.Z, self.atoms.symbol = get_atomic_number_symbol(Z=Z)
self.atoms.x = x
self.atoms.y = y
self.atoms.z = z
self._recalculate_cartn()
def __get_atomic_numbers(self):
"""Wrapper to get the atomic numbers from different structure classes"""
from javelin.utils import get_atomic_number_symbol
try: # ASE structure
return self.structure.get_atomic_numbers()
except AttributeError:
try: # diffpy structure
atomic_numbers, _ = get_atomic_number_symbol(
symbol=self.structure.element)
return atomic_numbers
except AttributeError:
raise ValueError("Unable to get elements from structure")
def add_atom(self, i=0, j=0, k=0, site=0, Z=None, symbol=None, position=None):
Z, symbol = get_atomic_number_symbol([Z], [symbol])
if position is None:
raise ValueError("position not provided")
self.atoms.loc[i, j, k, site] = [Z[0], symbol[0],
position[0], position[1], position[2]]
if self.rotations is not None:
self.rotations[i, j, k] = [1, 0, 0, 0]
if self.translations is not None:
self.translations[i, j, k] = [0, 0, 0]
def test_raises():
with pytest.raises(ValueError):
get_atomic_number_symbol()
with pytest.raises(ValueError):
get_atomic_number_symbol(symbol='A')
with pytest.raises(KeyError):
get_atomic_number_symbol(Z=1000)
def __init__(self, symbols=None, numbers=None, unitcell=1, ncells=None,
positions=None, rotations=False, translations=False, magnetic_moments=False):
if positions is not None:
numberOfAtoms = len(positions)
else:
numberOfAtoms = 0
if ncells is not None:
ncells = np.asarray(ncells)
if ncells is not None and positions is not None and ncells.prod() != numberOfAtoms:
raise ValueError("Product of ncells values doesn't equal length of positions")
if isinstance(unitcell, UnitCell):
self.unitcell = unitcell
else:
self.unitcell = UnitCell(unitcell)
miindex = get_miindex(numberOfAtoms, ncells)
self.atoms = DataFrame(index=miindex,
columns=['Z', 'symbol',
'x', 'y', 'z'])
if numbers is not None or symbols is not None:
self.atoms.Z, self.atoms.symbol = get_atomic_number_symbol(Z=numbers, symbol=symbols)
positions = np.asarray(positions)
self.atoms[['x', 'y', 'z']] = positions
if rotations:
self.rotations = DataFrame(index=miindex.droplevel(3),
columns=['w', 'x', 'y', 'z'])
else:
self.rotations = None
if translations:
self.translations = DataFrame(index=miindex.droplevel(3),
columns=['x', 'y', 'z'])
else:
self.translations = None
if magnetic_moments:
self.magmons = DataFrame(index=miindex,
columns=['spinx', 'spiny', 'spinz'])
else:
self.magmons = None
def add_atom(self,
i=0,
j=0,
k=0,
site=0,
Z=None,
symbol=None,
position=None):
Z, symbol = get_atomic_number_symbol([Z], [symbol])
if position is None:
raise ValueError("position not provided")
cartn = self.unitcell.cartesian(position)[0]
self.atoms.loc[i, j, k, site] = [
Z[0], symbol[0], position[0], position[1], position[2], cartn[0],
cartn[1], cartn[2]
]
if self.rotations is not None:
self.rotations[i, j, k] = [1, 0, 0, 0]
if self.translations is not None:
self.translations[i, j, k] = [0, 0, 0]
def __init__(self,
symbols=None,
numbers=None,
unitcell=1,
ncells=None,
positions=None,
rotations=False,
translations=False,
magnetic_moments=False):
if positions is not None:
numberOfAtoms = len(positions)
else:
numberOfAtoms = 0
if ncells is not None:
ncells = np.asarray(ncells)
if ncells is not None and positions is not None and ncells.prod(
) != numberOfAtoms:
raise ValueError(
"Product of ncells values doesn't equal length of positions")
if isinstance(unitcell, UnitCell):
self.unitcell = unitcell
else:
self.unitcell = UnitCell(unitcell)
miindex = get_miindex(numberOfAtoms, ncells)
self.atoms = DataFrame(index=miindex,
columns=[
'Z', 'symbol', 'x', 'y', 'z', 'cartn_x',
'cartn_y', 'cartn_z'
])
if numbers is not None or symbols is not None:
self.atoms.Z, self.atoms.symbol = get_atomic_number_symbol(
Z=numbers, symbol=symbols)
positions = np.asarray(positions)
self.atoms[['x', 'y', 'z']] = positions
if rotations:
self.rotations = DataFrame(index=miindex.droplevel(3),
columns=['w', 'x', 'y', 'z'])
else:
self.rotations = None
if translations:
self.translations = DataFrame(index=miindex.droplevel(3),
columns=['x', 'y', 'z'])
else:
self.translations = None
if magnetic_moments:
self.magmons = DataFrame(index=miindex,
columns=['spinx', 'spiny', 'spinz'])
else:
self.magmons = None
self._recalculate_cartn()